This is an interactive table of the covariate data.
The principal component analysis plot shown below was generated using the most varying 500 genes across all samples.
The expression values are obtained by the “vst” method, where the normalisation doesn’t take into account the experimental design.
In presence of strong biological signal, the samples should cluster with the biological condition. When samples are clustered according to other effects (for example patient, or technical batch), great care must be used when interpreting the results, as the other effects will considerably reduce the ability to extract meaningful biological information.
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## Warning: `arrange_()` is deprecated as of dplyr 0.7.0.
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The hierarchical clustering shown below was generated using the most varying 500 genes across all samples. The expression values are obtained by the “vst” method, where the normalisation doesn’t take into account the experimental design. The clustering is using euclidian distance for both the rows (genes) and columns (samples). In both cases, the distance between clusters is defined as the maximum of the distances between elements pairs from each cluster.
The hierarchical clustering can provide clues on which groups of genes could affect the clustering of samples.
The hierarchical clustering shown below was generated using all the full normalised dataset (15979 genes). The expression values are obtained by the “vst” method, where the normalisation doesn’t take into account the experimental design. The clustering is using euclidian distance for both the rows (genes) and columns (samples). In both cases, the distance between clusters is defined as the maximum of the distances between elements pairs from each cluster.
The expression values are obtained by the “vst” method, where the experimental design has been used for normalisation.
Contrasts generated by the pipeline.
A MA plot of the contrast other.
An interactive data table of the contrast results for other. Only results with adjusted p value smaller than 0.1 are included (total 7071 results shown).
## Warning in instance$preRenderHook(instance): It seems your data is too big for client-side DataTables. You may consider server-side processing: https://rstudio.github.io/
## DT/server.html
tmod enrichment analysis for otherTable. Summary of the results for contrast other shows number of significant gene sets at various significance levels and for AUC > 0.65.
| DB | 0.01 | 0.001 | 1e-04 | 1e-06 |
|---|---|---|---|---|
| tmod | 44 | 32 | 25 | 17 |
| msigdb_reactome | 15 | 12 | 10 | 6 |
| msigdb_hallmark | 3 | 3 | 3 | 3 |
| msigdb_kegg | 10 | 8 | 6 | 6 |
| msigdb_mir | 0 | 0 | 0 | 0 |
| msigdb_go_bp | 123 | 74 | 47 | 25 |
Table. Results of the tmod enrichment analysis for contrast other. Only significantly enriched gene sets are shown (FDR < 0.01, AUC > 0.65). AUC, area under curve; p.value, p-value from enrichment test; FDR, p-value corrected for multiple testing with Benjamini-Hochberg method.
No results at the specified thresholds
Fig. Upset plot.
Too few results to generate upset plot.
Dot plot for cluster profiler results for contrast other.
Enrichment map for cluster profiler results for contrast other.
UpSet plot for cluster profiler results for contrast other.
A MA plot of the contrast SC2.
An interactive data table of the contrast results for SC2. Only results with adjusted p value smaller than 0.1 are included (total 4011 results shown).
tmod enrichment analysis for SC2Table. Summary of the results for contrast SC2 shows number of significant gene sets at various significance levels and for AUC > 0.65.
| DB | 0.01 | 0.001 | 1e-04 | 1e-06 |
|---|---|---|---|---|
| tmod | 69 | 38 | 31 | 21 |
| msigdb_reactome | 68 | 55 | 46 | 30 |
| msigdb_hallmark | 6 | 6 | 6 | 6 |
| msigdb_kegg | 12 | 11 | 11 | 2 |
| msigdb_mir | 0 | 0 | 0 | 0 |
| msigdb_go_bp | 165 | 96 | 62 | 36 |
Table. Results of the tmod enrichment analysis for contrast SC2. Only significantly enriched gene sets are shown (FDR < 0.01, AUC > 0.65). AUC, area under curve; p.value, p-value from enrichment test; FDR, p-value corrected for multiple testing with Benjamini-Hochberg method.
No results at the specified thresholds
Fig. Upset plot.
Too few results to generate upset plot.
Dot plot for cluster profiler results for contrast SC2.
Enrichment map for cluster profiler results for contrast SC2.
UpSet plot for cluster profiler results for contrast SC2.
A MA plot of the contrast SC2_vs_other.
An interactive data table of the contrast results for SC2_vs_other. Only results with adjusted p value smaller than 0.1 are included (total 8473 results shown).
## Warning in instance$preRenderHook(instance): It seems your data is too big for client-side DataTables. You may consider server-side processing: https://rstudio.github.io/
## DT/server.html
tmod enrichment analysis for SC2_vs_otherTable. Summary of the results for contrast SC2_vs_other shows number of significant gene sets at various significance levels and for AUC > 0.65.
| DB | 0.01 | 0.001 | 1e-04 | 1e-06 |
|---|---|---|---|---|
| tmod | 55 | 38 | 23 | 14 |
| msigdb_reactome | 11 | 4 | 4 | 3 |
| msigdb_hallmark | 3 | 3 | 3 | 3 |
| msigdb_kegg | 1 | 1 | 0 | 0 |
| msigdb_mir | 0 | 0 | 0 | 0 |
| msigdb_go_bp | 105 | 47 | 29 | 12 |
Table. Results of the tmod enrichment analysis for contrast SC2_vs_other. Only significantly enriched gene sets are shown (FDR < 0.01, AUC > 0.65). AUC, area under curve; p.value, p-value from enrichment test; FDR, p-value corrected for multiple testing with Benjamini-Hochberg method.
No results at the specified thresholds
Fig. Upset plot.
Too few results to generate upset plot.
Dot plot for cluster profiler results for contrast SC2_vs_other.
Enrichment map for cluster profiler results for contrast SC2_vs_other.
Error in emapplot.enrichResult(x, showCategory = showCategory, color = color, : no enriched term found…
UpSet plot for cluster profiler results for contrast SC2_vs_other.
Error in [.data.frame(d, , 2) : undefined columns selected
Table. Overview of the databases for which gene set enrichment using tmod was performed.
| ID | Name | Description | TaxonID | N |
|---|---|---|---|---|
| tmod | Co-expression gene sets (tmod) | Gene sets derived from clustering expression profiles from human blood collected for various immune conditions. These gene sets are included in the tmod package by default. Check tmod documentation for further information. | 9606 | 606 |
| msigdb_reactome | Reactome gene sets (MSigDB) | Reactome gene sets the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/). | 9606 | 1532 |
| msigdb_hallmark | Hallmark gene sets (MSigDB) | Hallmark gene sets the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/). | 9606 | 50 |
| msigdb_kegg | KEGG pathways (MSigDB) | KEGG pathways from the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/). | 9606 | 186 |
| msigdb_mir | MIR targets (MSigDB) | MIR targets from the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/). | 9606 | 2377 |
| msigdb_go_bp | GO Biological Process (MSigDB) | GO Biological Process definitions from the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/). | 9606 | 7530 |
Database ID: tmod.
Description: Gene sets derived from clustering expression profiles from human blood collected for various immune conditions. These gene sets are included in the tmod package by default. Check tmod documentation for further information..
Tab. Summary of the results. Numbers show the number of enrichments significant at a given threshold for the given contrast and test type.
| Contrast | 0.05 | 0.01 | 0.001 | 1e-05 |
|---|---|---|---|---|
| other_ID0.pval | 59 | 48 | 33 | 22 |
| SC2_ID1.pval | 113 | 82 | 44 | 30 |
| SC2_vs_other_ID2.pval | 106 | 70 | 46 | 23 |
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
Fig. Panel plot showing results for the database tmod.
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
Figures below show the evidence plots for the top 5 gene sets. Each row corresponds to one gene set. Each column corresponds to one enrichment test (contrast + ordering). Each evidence plot shows the existing evidence for the enrichment of the given gene set in the given contrast. The curve shows the Receiver Operator Characteristic (ROC) curve for a given gene set. The rug below the figure represents the ordered list of genes. Genes belonging to a given gene set are highlighted. Colors indicate whether the genes are positively or negatively regulated (red or blue, respectively), while color brightness indicates whether genes are significantly regulated (at q < 0.05).
Database ID: msigdb_reactome.
Description: Reactome gene sets the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/)..
Tab. Summary of the results. Numbers show the number of enrichments significant at a given threshold for the given contrast and test type.
| Contrast | 0.05 | 0.01 | 0.001 | 1e-05 |
|---|---|---|---|---|
| other_ID0.pval | 49 | 31 | 20 | 12 |
| SC2_ID1.pval | 228 | 182 | 148 | 77 |
| SC2_vs_other_ID2.pval | 68 | 40 | 17 | 9 |
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
Fig. Panel plot showing results for the database msigdb_reactome.
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
Figures below show the evidence plots for the top 5 gene sets. Each row corresponds to one gene set. Each column corresponds to one enrichment test (contrast + ordering). Each evidence plot shows the existing evidence for the enrichment of the given gene set in the given contrast. The curve shows the Receiver Operator Characteristic (ROC) curve for a given gene set. The rug below the figure represents the ordered list of genes. Genes belonging to a given gene set are highlighted. Colors indicate whether the genes are positively or negatively regulated (red or blue, respectively), while color brightness indicates whether genes are significantly regulated (at q < 0.05).
Database ID: msigdb_hallmark.
Description: Hallmark gene sets the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/)..
Tab. Summary of the results. Numbers show the number of enrichments significant at a given threshold for the given contrast and test type.
| Contrast | 0.05 | 0.01 | 0.001 | 1e-05 |
|---|---|---|---|---|
| other_ID0.pval | 14 | 12 | 10 | 8 |
| SC2_ID1.pval | 21 | 13 | 13 | 11 |
| SC2_vs_other_ID2.pval | 24 | 19 | 13 | 11 |
Fig. Panel plot showing results for the database msigdb_hallmark.
Figures below show the evidence plots for the top 5 gene sets. Each row corresponds to one gene set. Each column corresponds to one enrichment test (contrast + ordering). Each evidence plot shows the existing evidence for the enrichment of the given gene set in the given contrast. The curve shows the Receiver Operator Characteristic (ROC) curve for a given gene set. The rug below the figure represents the ordered list of genes. Genes belonging to a given gene set are highlighted. Colors indicate whether the genes are positively or negatively regulated (red or blue, respectively), while color brightness indicates whether genes are significantly regulated (at q < 0.05).
Database ID: msigdb_kegg.
Description: KEGG pathways from the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/)..
Tab. Summary of the results. Numbers show the number of enrichments significant at a given threshold for the given contrast and test type.
| Contrast | 0.05 | 0.01 | 0.001 | 1e-05 |
|---|---|---|---|---|
| other_ID0.pval | 24 | 22 | 15 | 8 |
| SC2_ID1.pval | 30 | 20 | 16 | 9 |
| SC2_vs_other_ID2.pval | 19 | 7 | 6 | 2 |
Fig. Panel plot showing results for the database msigdb_kegg.
Figures below show the evidence plots for the top 5 gene sets. Each row corresponds to one gene set. Each column corresponds to one enrichment test (contrast + ordering). Each evidence plot shows the existing evidence for the enrichment of the given gene set in the given contrast. The curve shows the Receiver Operator Characteristic (ROC) curve for a given gene set. The rug below the figure represents the ordered list of genes. Genes belonging to a given gene set are highlighted. Colors indicate whether the genes are positively or negatively regulated (red or blue, respectively), while color brightness indicates whether genes are significantly regulated (at q < 0.05).
Database ID: msigdb_mir.
Description: MIR targets from the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/)..
Tab. Summary of the results. Numbers show the number of enrichments significant at a given threshold for the given contrast and test type.
| Contrast | 0.05 | 0.01 | 0.001 | 1e-05 |
|---|---|---|---|---|
| other_ID0.pval | 0 | 0 | 0 | 0 |
| SC2_ID1.pval | 0 | 0 | 0 | 0 |
| SC2_vs_other_ID2.pval | 0 | 0 | 0 | 0 |
No figure produced because there were less than 2 significant results enrichment results.
Database ID: msigdb_go_bp.
Description: GO Biological Process definitions from the Molecular Signatures DB (https://www.gsea-msigdb.org/gsea/msigdb/)..
Tab. Summary of the results. Numbers show the number of enrichments significant at a given threshold for the given contrast and test type.
| Contrast | 0.05 | 0.01 | 0.001 | 1e-05 |
|---|---|---|---|---|
| other_ID0.pval | 563 | 367 | 220 | 118 |
| SC2_ID1.pval | 885 | 599 | 383 | 193 |
| SC2_vs_other_ID2.pval | 766 | 465 | 275 | 125 |
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
Fig. Panel plot showing results for the database msigdb_go_bp.
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
## Warning in max(x, na.rm = T): no non-missing arguments to max; returning -Inf
Figures below show the evidence plots for the top 5 gene sets. Each row corresponds to one gene set. Each column corresponds to one enrichment test (contrast + ordering). Each evidence plot shows the existing evidence for the enrichment of the given gene set in the given contrast. The curve shows the Receiver Operator Characteristic (ROC) curve for a given gene set. The rug below the figure represents the ordered list of genes. Genes belonging to a given gene set are highlighted. Colors indicate whether the genes are positively or negatively regulated (red or blue, respectively), while color brightness indicates whether genes are significantly regulated (at q < 0.05).
Table. Overview of the databases for which gene set enrichment using cluster_profiler was performed.
Fig. Panel plot showing results for the database MSigDb.H. Effect size is the normalized enrichment score (NES). Blue color indicates negative enrichment score, red color indicates positive NES. Size of the dots corresponds to the magnitude of NES as shown in the legend. Color intensity indicates p-value.
Fig. Panel plot showing results for the database MSigDb.C2. Effect size is the normalized enrichment score (NES). Blue color indicates negative enrichment score, red color indicates positive NES. Size of the dots corresponds to the magnitude of NES as shown in the legend. Color intensity indicates p-value.
Fig. Panel plot showing results for the database GO.BP. Effect size is the relative enrichment score (E) defined as (b/n)/(B/N), where b is the number of significant genes in the given gene set, n is total number of genes in the given gene set, B is the total number of significant genes and N is the total number of genes. Size of the dots corresponds to the magnitude of E as shown in the legend. Color intensity indicates p-value.
Fig. Panel plot showing results for the database GO.MF. Effect size is the relative enrichment score (E) defined as (b/n)/(B/N), where b is the number of significant genes in the given gene set, n is total number of genes in the given gene set, B is the total number of significant genes and N is the total number of genes. Size of the dots corresponds to the magnitude of E as shown in the legend. Color intensity indicates p-value.
Fig. Panel plot showing results for the database KEGG.pathways. Effect size is the relative enrichment score (E) defined as (b/n)/(B/N), where b is the number of significant genes in the given gene set, n is total number of genes in the given gene set, B is the total number of significant genes and N is the total number of genes. Size of the dots corresponds to the magnitude of E as shown in the legend. Color intensity indicates p-value.
Table. Following files have been exported to the export_files directory.
| Description |
|---|
| Raw counts, log CPM and rlog counts |
| Results of differential expression analysis for all contrasts |
| Results of gene enrichment analysis with tmod for contrast other_ID0 |
| Results of gene enrichment analysis with tmod for contrast SC2_ID1 |
| Results of gene enrichment analysis with tmod for contrast SC2_vs_other_ID2 |
| File |
|---|
| counts.xlsx |
| differential_expression_results.xlsx |
| tmod.other_ID0.xlsx |
| tmod.SC2_ID1.xlsx |
| tmod.SC2_vs_other_ID2.xlsx |
## R version 3.6.1 (2019-07-05)
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## [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
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## [21] dplyr_1.0.0 magrittr_1.5 DT_0.14 yaml_2.2.1 DESeq2_1.26.0
## [26] SummarizedExperiment_1.16.1 DelayedArray_0.12.3 BiocParallel_1.20.1 matrixStats_0.56.0 Biobase_2.46.0
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